Multiple sequence alignment - TraesCS2A01G307600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G307600 chr2A 100.000 4693 0 0 1 4693 528659207 528654515 0.000000e+00 8667
1 TraesCS2A01G307600 chr2D 89.787 2017 91 51 1988 3926 391716637 391714658 0.000000e+00 2477
2 TraesCS2A01G307600 chr2D 92.447 662 23 8 1 637 391720179 391719520 0.000000e+00 920
3 TraesCS2A01G307600 chr2D 90.534 655 33 13 725 1360 391717860 391717216 0.000000e+00 839
4 TraesCS2A01G307600 chr2D 95.122 287 11 3 3926 4210 391714628 391714343 2.580000e-122 449
5 TraesCS2A01G307600 chr2D 91.532 248 10 7 1720 1963 391716864 391716624 9.730000e-87 331
6 TraesCS2A01G307600 chr2D 90.717 237 12 3 638 868 391719421 391719189 1.640000e-79 307
7 TraesCS2A01G307600 chr2D 86.758 219 16 6 1430 1640 391717111 391716898 1.020000e-56 231
8 TraesCS2A01G307600 chr2D 96.939 98 3 0 4596 4693 391713948 391713851 1.040000e-36 165
9 TraesCS2A01G307600 chr2B 89.959 1972 95 40 2017 3926 463279924 463277994 0.000000e+00 2449
10 TraesCS2A01G307600 chr2B 84.578 1660 87 72 377 1963 463281628 463280065 0.000000e+00 1491
11 TraesCS2A01G307600 chr2B 86.517 534 54 5 4162 4693 463277590 463277073 5.270000e-159 571
12 TraesCS2A01G307600 chr2B 82.869 251 26 9 3 242 463281955 463281711 4.760000e-50 209
13 TraesCS2A01G307600 chr2B 86.127 173 23 1 3926 4098 463277964 463277793 8.020000e-43 185


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G307600 chr2A 528654515 528659207 4692 True 8667.000 8667 100.0000 1 4693 1 chr2A.!!$R1 4692
1 TraesCS2A01G307600 chr2D 391713851 391720179 6328 True 714.875 2477 91.7295 1 4693 8 chr2D.!!$R1 4692
2 TraesCS2A01G307600 chr2B 463277073 463281955 4882 True 981.000 2449 86.0100 3 4693 5 chr2B.!!$R1 4690

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
713 843 0.811281 GAGGGTGCGGGAGAATTTTG 59.189 55.0 0.0 0.0 0.00 2.44 F
1633 3331 0.036294 CCCTCACTCTCGGGGTTTTC 60.036 60.0 0.0 0.0 36.78 2.29 F
2337 4201 0.107703 GGTGACGAATGAGCCATGGA 60.108 55.0 18.4 0.0 0.00 3.41 F
2952 4839 0.537188 GGCGATGGTGGAGAAAGAGA 59.463 55.0 0.0 0.0 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2612 4493 0.319297 ACAGTAAGTTCGTGCCGTCC 60.319 55.0 0.00 0.00 0.00 4.79 R
3327 5242 0.032678 CAGGACAAGCGTCTGTCTGT 59.967 55.0 15.60 1.86 44.33 3.41 R
3328 5243 0.315251 TCAGGACAAGCGTCTGTCTG 59.685 55.0 15.60 12.35 44.33 3.51 R
4453 6580 0.039798 TAAGTGACGACGTGGACAGC 60.040 55.0 4.58 0.00 0.00 4.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 114 5.310451 TGTTTACCATCAGTTGTAACCCTC 58.690 41.667 0.00 0.00 0.00 4.30
195 216 4.155709 TGGTGCCAAAAATACATCTGGAA 58.844 39.130 0.00 0.00 0.00 3.53
239 267 6.280643 CAATTATGTACCGAGTGAATGGAGA 58.719 40.000 0.00 0.00 0.00 3.71
250 278 6.294176 CCGAGTGAATGGAGACTTTGAAATTT 60.294 38.462 0.00 0.00 0.00 1.82
263 291 4.769345 TTGAAATTTCCAACAAAGCCCT 57.231 36.364 15.48 0.00 0.00 5.19
264 292 4.070630 TGAAATTTCCAACAAAGCCCTG 57.929 40.909 15.48 0.00 0.00 4.45
374 402 2.159181 GCGTTGTGCATCTACCGTT 58.841 52.632 0.00 0.00 45.45 4.44
405 433 6.168389 CAACTATGGCATATGCATCAGTCTA 58.832 40.000 28.07 7.59 44.36 2.59
409 437 3.259123 TGGCATATGCATCAGTCTATCGT 59.741 43.478 28.07 0.00 44.36 3.73
506 535 4.806247 CCAGTCGACCAGATAAATTGTCTC 59.194 45.833 13.01 0.00 0.00 3.36
593 625 1.273048 GGCATTTGTGTTCAGGCATCA 59.727 47.619 0.00 0.00 0.00 3.07
594 626 2.331194 GCATTTGTGTTCAGGCATCAC 58.669 47.619 0.00 0.00 0.00 3.06
669 799 1.495878 AGCTTATCGCGATGCAGAAG 58.504 50.000 31.05 24.80 45.59 2.85
713 843 0.811281 GAGGGTGCGGGAGAATTTTG 59.189 55.000 0.00 0.00 0.00 2.44
723 853 1.327764 GGAGAATTTTGCCGCGTAGAG 59.672 52.381 4.92 0.00 0.00 2.43
750 2358 6.753107 TCTACTATTGCTTAAACAAAGGGC 57.247 37.500 0.00 0.00 35.58 5.19
788 2396 4.883021 AGGAGAGGATTGAGTGTACCTA 57.117 45.455 0.00 0.00 32.53 3.08
914 2532 2.224867 CCTCTCTCATCTCTCCCTCTCC 60.225 59.091 0.00 0.00 0.00 3.71
918 2536 0.856982 TCATCTCTCCCTCTCCCTCC 59.143 60.000 0.00 0.00 0.00 4.30
927 2545 0.820871 CCTCTCCCTCCGAAGTCTTG 59.179 60.000 0.00 0.00 0.00 3.02
931 2549 0.903454 TCCCTCCGAAGTCTTGACCC 60.903 60.000 0.00 0.00 0.00 4.46
973 2591 1.327303 TGGCTTGCTGTTAGTTTGGG 58.673 50.000 0.00 0.00 0.00 4.12
974 2592 1.328279 GGCTTGCTGTTAGTTTGGGT 58.672 50.000 0.00 0.00 0.00 4.51
984 2602 0.981183 TAGTTTGGGTCGGCACTCAT 59.019 50.000 0.00 0.00 31.02 2.90
986 2604 0.889186 GTTTGGGTCGGCACTCATGT 60.889 55.000 0.00 0.00 31.02 3.21
1015 2633 2.092753 GCTTTGATGATGGTGGAGAGGA 60.093 50.000 0.00 0.00 0.00 3.71
1042 2660 1.304282 GAGGGAGAAGCAATGGCCA 59.696 57.895 8.56 8.56 42.56 5.36
1068 2686 4.082523 CCGCGGCAGGAAGGAGAA 62.083 66.667 14.67 0.00 0.00 2.87
1069 2687 2.510238 CGCGGCAGGAAGGAGAAG 60.510 66.667 0.00 0.00 0.00 2.85
1070 2688 2.821810 GCGGCAGGAAGGAGAAGC 60.822 66.667 0.00 0.00 0.00 3.86
1077 2695 0.617935 AGGAAGGAGAAGCAGAAGCC 59.382 55.000 0.00 0.00 43.56 4.35
1079 2697 1.365368 GAAGGAGAAGCAGAAGCCGC 61.365 60.000 0.00 0.00 43.56 6.53
1080 2698 1.835927 AAGGAGAAGCAGAAGCCGCT 61.836 55.000 0.00 0.00 43.56 5.52
1122 2752 0.633921 CAGGAGAGAAGGGAGAGGGA 59.366 60.000 0.00 0.00 0.00 4.20
1143 2773 1.410882 GAGAGGGATGACGGAGAAAGG 59.589 57.143 0.00 0.00 0.00 3.11
1145 2775 1.153147 GGGATGACGGAGAAAGGGC 60.153 63.158 0.00 0.00 0.00 5.19
1168 2798 4.214327 GCGAGGAGCGGAAGGAGG 62.214 72.222 0.00 0.00 41.29 4.30
1190 2820 0.333312 AGCGAGGAGGAAGAAGAGGA 59.667 55.000 0.00 0.00 0.00 3.71
1234 2864 1.216710 CTGGAAGAGTGGTCCGAGC 59.783 63.158 0.00 0.00 38.06 5.03
1406 3075 2.006805 TGGTGTTCATTTGGCATCCA 57.993 45.000 0.00 0.00 0.00 3.41
1444 3122 0.878523 TCGGTTTCTTGACGTGCCTG 60.879 55.000 0.00 0.00 0.00 4.85
1448 3126 1.003866 GTTTCTTGACGTGCCTGTGTC 60.004 52.381 0.00 0.00 35.67 3.67
1449 3127 0.464036 TTCTTGACGTGCCTGTGTCT 59.536 50.000 0.00 0.00 36.10 3.41
1450 3128 0.249447 TCTTGACGTGCCTGTGTCTG 60.249 55.000 0.00 0.00 36.10 3.51
1452 3130 0.809636 TTGACGTGCCTGTGTCTGTG 60.810 55.000 0.00 0.00 36.10 3.66
1453 3131 2.588877 ACGTGCCTGTGTCTGTGC 60.589 61.111 0.00 0.00 0.00 4.57
1463 3141 1.242076 GTGTCTGTGCATCTTTGGCT 58.758 50.000 0.00 0.00 0.00 4.75
1473 3151 2.670509 GCATCTTTGGCTTGTTGCTCTC 60.671 50.000 0.00 0.00 42.39 3.20
1481 3159 0.951040 CTTGTTGCTCTCCCGTCCAC 60.951 60.000 0.00 0.00 0.00 4.02
1509 3188 1.364626 GGTCCTTGCTGTCGCTGATG 61.365 60.000 0.00 0.00 36.97 3.07
1598 3277 5.054477 CCAACGGAACATCGAGGTAAATAT 58.946 41.667 1.83 0.00 0.00 1.28
1605 3284 7.961827 CGGAACATCGAGGTAAATATACTACTC 59.038 40.741 1.83 0.00 32.36 2.59
1606 3285 9.012161 GGAACATCGAGGTAAATATACTACTCT 57.988 37.037 1.83 0.00 32.36 3.24
1608 3287 9.796180 AACATCGAGGTAAATATACTACTCTCT 57.204 33.333 1.83 0.00 32.36 3.10
1609 3288 9.796180 ACATCGAGGTAAATATACTACTCTCTT 57.204 33.333 0.00 0.00 32.36 2.85
1611 3290 8.845413 TCGAGGTAAATATACTACTCTCTTCC 57.155 38.462 0.00 0.00 32.36 3.46
1612 3291 7.882271 TCGAGGTAAATATACTACTCTCTTCCC 59.118 40.741 0.00 0.00 32.36 3.97
1633 3331 0.036294 CCCTCACTCTCGGGGTTTTC 60.036 60.000 0.00 0.00 36.78 2.29
1634 3332 0.389948 CCTCACTCTCGGGGTTTTCG 60.390 60.000 0.00 0.00 0.00 3.46
1635 3333 0.317479 CTCACTCTCGGGGTTTTCGT 59.683 55.000 0.00 0.00 0.00 3.85
1636 3334 1.542915 CTCACTCTCGGGGTTTTCGTA 59.457 52.381 0.00 0.00 0.00 3.43
1637 3335 1.962807 TCACTCTCGGGGTTTTCGTAA 59.037 47.619 0.00 0.00 0.00 3.18
1638 3336 2.029649 TCACTCTCGGGGTTTTCGTAAG 60.030 50.000 0.00 0.00 0.00 2.34
1639 3337 1.966354 ACTCTCGGGGTTTTCGTAAGT 59.034 47.619 0.00 0.00 39.48 2.24
1640 3338 3.057315 CACTCTCGGGGTTTTCGTAAGTA 60.057 47.826 0.00 0.00 39.48 2.24
1641 3339 3.192212 ACTCTCGGGGTTTTCGTAAGTAG 59.808 47.826 0.00 0.00 39.48 2.57
1642 3340 3.157087 TCTCGGGGTTTTCGTAAGTAGT 58.843 45.455 0.00 0.00 39.48 2.73
1643 3341 4.331968 TCTCGGGGTTTTCGTAAGTAGTA 58.668 43.478 0.00 0.00 39.48 1.82
1644 3342 4.156008 TCTCGGGGTTTTCGTAAGTAGTAC 59.844 45.833 0.00 0.00 39.48 2.73
1658 3356 7.006187 GTAAGTAGTACGTACCACTAGGAAC 57.994 44.000 23.95 16.26 38.69 3.62
1659 3357 5.428184 AGTAGTACGTACCACTAGGAACT 57.572 43.478 22.72 10.61 38.69 3.01
1660 3358 6.546428 AGTAGTACGTACCACTAGGAACTA 57.454 41.667 22.72 4.38 38.69 2.24
1689 3389 3.180417 GCGATCTAGCTAAATTGCTGC 57.820 47.619 11.46 0.00 43.87 5.25
1691 3391 3.363772 GCGATCTAGCTAAATTGCTGCTG 60.364 47.826 11.46 0.00 43.87 4.41
1703 3405 7.383843 GCTAAATTGCTGCTGGTAAAAACTAAA 59.616 33.333 0.00 0.00 0.00 1.85
1706 3408 5.782893 TGCTGCTGGTAAAAACTAAACAT 57.217 34.783 0.00 0.00 0.00 2.71
1708 3410 4.385748 GCTGCTGGTAAAAACTAAACATGC 59.614 41.667 0.00 0.00 0.00 4.06
1711 3413 4.381566 GCTGGTAAAAACTAAACATGCACG 59.618 41.667 0.00 0.00 0.00 5.34
1712 3414 5.752892 TGGTAAAAACTAAACATGCACGA 57.247 34.783 0.00 0.00 0.00 4.35
1713 3415 6.132791 TGGTAAAAACTAAACATGCACGAA 57.867 33.333 0.00 0.00 0.00 3.85
1714 3416 6.202937 TGGTAAAAACTAAACATGCACGAAG 58.797 36.000 0.00 0.00 0.00 3.79
1715 3417 5.116528 GGTAAAAACTAAACATGCACGAAGC 59.883 40.000 0.00 0.00 45.96 3.86
1730 3432 1.486211 GAAGCAGTAGTAGGCAGGGA 58.514 55.000 0.00 0.00 0.00 4.20
1746 3448 1.677637 GGGAGTCTCGATCACACCCC 61.678 65.000 15.47 11.81 38.41 4.95
1747 3449 0.684805 GGAGTCTCGATCACACCCCT 60.685 60.000 0.00 0.00 0.00 4.79
1763 3465 1.834263 CCCCTCTACCTGAGACCAAAG 59.166 57.143 0.00 0.00 45.39 2.77
1774 3476 5.072741 CCTGAGACCAAAGATCCAAAAGAA 58.927 41.667 0.00 0.00 0.00 2.52
1788 3490 3.365364 CCAAAAGAAGATGGCAAGTCGAC 60.365 47.826 7.70 7.70 0.00 4.20
1856 3558 1.134610 GTGGTCCACGTAATACCCTGG 60.135 57.143 6.18 0.00 31.97 4.45
1873 3575 2.305009 CTGGCTTTTCCCATCCATCTC 58.695 52.381 0.00 0.00 33.64 2.75
1874 3576 1.312815 GGCTTTTCCCATCCATCTCG 58.687 55.000 0.00 0.00 0.00 4.04
1875 3577 1.408822 GGCTTTTCCCATCCATCTCGT 60.409 52.381 0.00 0.00 0.00 4.18
1876 3578 1.943340 GCTTTTCCCATCCATCTCGTC 59.057 52.381 0.00 0.00 0.00 4.20
1877 3579 2.565841 CTTTTCCCATCCATCTCGTCC 58.434 52.381 0.00 0.00 0.00 4.79
1919 3621 0.326595 TAGGCGCCAAAAGTGATGGA 59.673 50.000 31.54 0.00 40.56 3.41
1945 3648 2.427095 CCTGTGGCCTGCTTATTTTACC 59.573 50.000 3.32 0.00 0.00 2.85
1950 3653 4.335594 GTGGCCTGCTTATTTTACCTAGTG 59.664 45.833 3.32 0.00 0.00 2.74
1951 3654 4.018779 TGGCCTGCTTATTTTACCTAGTGT 60.019 41.667 3.32 0.00 0.00 3.55
1954 3657 6.771267 GGCCTGCTTATTTTACCTAGTGTTAT 59.229 38.462 0.00 0.00 0.00 1.89
1955 3658 7.041303 GGCCTGCTTATTTTACCTAGTGTTATC 60.041 40.741 0.00 0.00 0.00 1.75
1956 3659 7.715686 GCCTGCTTATTTTACCTAGTGTTATCT 59.284 37.037 0.00 0.00 0.00 1.98
1957 3660 9.046296 CCTGCTTATTTTACCTAGTGTTATCTG 57.954 37.037 0.00 0.00 0.00 2.90
1958 3661 9.817809 CTGCTTATTTTACCTAGTGTTATCTGA 57.182 33.333 0.00 0.00 0.00 3.27
1959 3662 9.817809 TGCTTATTTTACCTAGTGTTATCTGAG 57.182 33.333 0.00 0.00 0.00 3.35
1960 3663 8.766151 GCTTATTTTACCTAGTGTTATCTGAGC 58.234 37.037 0.00 0.00 0.00 4.26
1984 3687 8.983307 GCTATATAAGCGTGGTTATTCTACTT 57.017 34.615 9.33 0.00 42.53 2.24
1985 3688 9.420551 GCTATATAAGCGTGGTTATTCTACTTT 57.579 33.333 9.33 0.00 42.53 2.66
2014 3717 9.700831 ATTTTCTGAGTTTAGCCTGGTTATTAT 57.299 29.630 0.00 0.00 0.00 1.28
2066 3894 3.906649 GAGCACGCGTCTGCATCG 61.907 66.667 21.73 5.34 42.97 3.84
2071 3899 4.829518 CGCGTCTGCATCGTCCGA 62.830 66.667 0.00 0.00 42.97 4.55
2089 3917 0.462047 GACGCATCACCCGATCCTTT 60.462 55.000 0.00 0.00 0.00 3.11
2090 3918 0.828022 ACGCATCACCCGATCCTTTA 59.172 50.000 0.00 0.00 0.00 1.85
2162 3991 1.674441 TCATTCGAGACCGCGATAGTT 59.326 47.619 8.23 0.00 40.35 2.24
2179 4008 3.199880 AGTTTGATCGGATCATGGGAC 57.800 47.619 20.53 15.68 39.39 4.46
2289 4150 5.574188 ACCATGGGATTAGGCAAATATCTC 58.426 41.667 18.09 0.00 0.00 2.75
2330 4194 1.361668 CGCAAGGGGTGACGAATGAG 61.362 60.000 0.00 0.00 0.00 2.90
2337 4201 0.107703 GGTGACGAATGAGCCATGGA 60.108 55.000 18.40 0.00 0.00 3.41
2338 4202 1.475751 GGTGACGAATGAGCCATGGAT 60.476 52.381 18.40 10.08 0.00 3.41
2339 4203 2.292267 GTGACGAATGAGCCATGGATT 58.708 47.619 18.40 6.37 0.00 3.01
2340 4204 3.466836 GTGACGAATGAGCCATGGATTA 58.533 45.455 18.40 6.37 0.00 1.75
2341 4205 3.496130 GTGACGAATGAGCCATGGATTAG 59.504 47.826 18.40 9.44 0.00 1.73
2342 4206 3.070018 GACGAATGAGCCATGGATTAGG 58.930 50.000 18.40 2.15 0.00 2.69
2415 4279 0.898320 ACATCCGTCCTCCTTCACAG 59.102 55.000 0.00 0.00 0.00 3.66
2474 4349 1.291132 CTTTGCTAGAAGCTACGGGC 58.709 55.000 0.00 0.00 42.97 6.13
2597 4476 2.280389 ATCGCACGGCTGCATAGG 60.280 61.111 0.50 0.00 44.50 2.57
2611 4492 4.848357 CTGCATAGGGTCCCTATAATTGG 58.152 47.826 27.24 16.74 44.19 3.16
2612 4493 3.591527 TGCATAGGGTCCCTATAATTGGG 59.408 47.826 27.24 16.09 44.19 4.12
2638 4519 4.164294 GGCACGAACTTACTGTAGTACTG 58.836 47.826 5.39 5.69 0.00 2.74
2641 4522 6.404074 GGCACGAACTTACTGTAGTACTGTAT 60.404 42.308 17.63 6.33 33.53 2.29
2642 4523 6.468319 GCACGAACTTACTGTAGTACTGTATG 59.532 42.308 21.60 21.60 33.53 2.39
2727 4611 1.067669 GTAGCGATGCAGACAGATGGA 59.932 52.381 0.00 0.00 0.00 3.41
2767 4652 8.791327 TTCAGCATTGACTCATCTATGTTTTA 57.209 30.769 0.00 0.00 39.45 1.52
2942 4829 1.807165 CACTCTGACGGCGATGGTG 60.807 63.158 16.62 10.99 0.00 4.17
2952 4839 0.537188 GGCGATGGTGGAGAAAGAGA 59.463 55.000 0.00 0.00 0.00 3.10
2993 4880 2.182842 GGCCGATAGCTGTGCAAGG 61.183 63.158 0.00 0.00 43.05 3.61
3028 4915 4.451900 CTCACTAGGTGAACCAACAAACT 58.548 43.478 1.62 0.00 42.26 2.66
3032 4919 4.821805 ACTAGGTGAACCAACAAACTGATG 59.178 41.667 1.62 0.00 38.89 3.07
3036 4923 3.551485 GTGAACCAACAAACTGATGCAAC 59.449 43.478 0.00 0.00 0.00 4.17
3037 4924 3.446873 TGAACCAACAAACTGATGCAACT 59.553 39.130 0.00 0.00 0.00 3.16
3038 4925 4.081752 TGAACCAACAAACTGATGCAACTT 60.082 37.500 0.00 0.00 0.00 2.66
3039 4926 5.126222 TGAACCAACAAACTGATGCAACTTA 59.874 36.000 0.00 0.00 0.00 2.24
3120 5018 8.969260 TTCATCTTCTTACTGTGCAATATCAT 57.031 30.769 0.00 0.00 0.00 2.45
3137 5035 7.339721 GCAATATCATCAGATCCATGGATTTCT 59.660 37.037 27.93 19.38 35.67 2.52
3208 5121 2.266627 GCAGAGCCTTGCACAGCTT 61.267 57.895 10.81 0.00 43.53 3.74
3241 5154 0.605589 ACAAGGTCTCTCTCAAGCCG 59.394 55.000 0.00 0.00 0.00 5.52
3283 5196 2.426406 GGCATGCAAGGTTAGGGGC 61.426 63.158 21.36 0.00 0.00 5.80
3286 5199 1.380380 ATGCAAGGTTAGGGGCTGC 60.380 57.895 0.00 0.00 0.00 5.25
3310 5225 3.968724 CAGTTTGTTTTTCAGCTAGCGAC 59.031 43.478 9.55 3.57 0.00 5.19
3337 5252 1.006102 AAAGCCCGACAGACAGACG 60.006 57.895 0.00 0.00 35.18 4.18
3354 5269 2.563179 AGACGCTTGTCCTGATAACACT 59.437 45.455 0.00 0.00 43.97 3.55
3371 5286 2.094752 ACACTTGGTTGACTTGCACAAC 60.095 45.455 9.56 9.56 44.40 3.32
3374 5289 0.455410 TGGTTGACTTGCACAACTGC 59.545 50.000 15.71 4.09 44.50 4.40
3406 5321 5.180367 TGTTGAAACAGATCGCATTGAAA 57.820 34.783 0.00 0.00 34.30 2.69
3471 5386 4.316645 GAAAACCAGAGTTACAGTCTCCC 58.683 47.826 0.00 0.00 34.19 4.30
3476 5391 1.903183 AGAGTTACAGTCTCCCCAAGC 59.097 52.381 0.00 0.00 32.93 4.01
3580 5497 2.073816 CGATCCCCGATTAATTTCCCG 58.926 52.381 0.00 0.00 41.76 5.14
3581 5498 1.810755 GATCCCCGATTAATTTCCCGC 59.189 52.381 0.00 0.00 0.00 6.13
3592 5509 0.604243 ATTTCCCGCGTGTTGCTACA 60.604 50.000 4.92 0.00 43.27 2.74
3648 5569 5.032863 GTGATTAAGCATTGCTGTGTGATC 58.967 41.667 12.82 8.99 39.62 2.92
3791 5718 2.727544 TTTTTGAGCTGCCCGTGC 59.272 55.556 0.00 0.00 38.26 5.34
3900 5836 7.819900 AGTCAATGTACTTGTCCATCTTTCTAC 59.180 37.037 0.00 0.00 36.20 2.59
3902 5838 5.416271 TGTACTTGTCCATCTTTCTACCC 57.584 43.478 0.00 0.00 0.00 3.69
3983 5949 2.567615 TGCTCTGAACTAAGGGAGGTTC 59.432 50.000 0.00 0.00 41.28 3.62
4056 6022 3.552875 GGGGTTTGCTAGGGTTTCTATC 58.447 50.000 0.00 0.00 0.00 2.08
4071 6037 6.402658 GGGTTTCTATCGCTCAAAGAGAAAAG 60.403 42.308 0.00 0.00 37.75 2.27
4172 6297 4.261801 TCCAAAGACTTTATAGCTGGTGC 58.738 43.478 0.00 0.00 40.05 5.01
4215 6340 9.405587 GTTTTGTTTTGCTATGCTAGTATTTGA 57.594 29.630 0.00 0.00 0.00 2.69
4225 6350 7.255801 GCTATGCTAGTATTTGACTCCTTCTCT 60.256 40.741 0.00 0.00 39.81 3.10
4226 6351 9.290988 CTATGCTAGTATTTGACTCCTTCTCTA 57.709 37.037 0.00 0.00 39.81 2.43
4291 6416 5.183140 ACCAAATTTATTGAGTTGGGAGACG 59.817 40.000 8.67 0.00 44.01 4.18
4299 6424 0.532862 AGTTGGGAGACGTGTGCAAG 60.533 55.000 6.53 0.00 0.00 4.01
4301 6426 0.249868 TTGGGAGACGTGTGCAAGAG 60.250 55.000 6.53 0.00 0.00 2.85
4317 6442 1.925972 GAGGGAGGGGGTGAGCTTT 60.926 63.158 0.00 0.00 0.00 3.51
4358 6483 9.734984 TTCAAATAGTCTAAGGAAAGGTAAAGG 57.265 33.333 0.00 0.00 0.00 3.11
4359 6484 8.887393 TCAAATAGTCTAAGGAAAGGTAAAGGT 58.113 33.333 0.00 0.00 0.00 3.50
4382 6507 8.683615 AGGTAAAAGTAAAAGAGACAAAACTGG 58.316 33.333 0.00 0.00 0.00 4.00
4387 6512 6.782150 AGTAAAAGAGACAAAACTGGAAACG 58.218 36.000 0.00 0.00 0.00 3.60
4388 6513 5.890424 AAAAGAGACAAAACTGGAAACGA 57.110 34.783 0.00 0.00 0.00 3.85
4398 6523 3.305398 ACTGGAAACGACATGAGAGAC 57.695 47.619 0.00 0.00 0.00 3.36
4409 6534 7.334844 ACGACATGAGAGACATAGTAAATGA 57.665 36.000 0.00 0.00 37.46 2.57
4422 6549 7.497595 ACATAGTAAATGATGCGAGAGGTAAA 58.502 34.615 0.00 0.00 0.00 2.01
4431 6558 3.211045 TGCGAGAGGTAAATAAATGCCC 58.789 45.455 0.00 0.00 0.00 5.36
4468 6595 2.178892 CTACGCTGTCCACGTCGTCA 62.179 60.000 0.70 0.00 43.88 4.35
4484 6611 1.226746 GTCACTTAAGTGGCTTGCGT 58.773 50.000 28.75 0.00 46.41 5.24
4488 6615 2.157668 CACTTAAGTGGCTTGCGTACTG 59.842 50.000 25.19 0.00 42.10 2.74
4511 6638 2.421739 CCCGGTTCATCCTAGCCG 59.578 66.667 0.00 0.00 43.40 5.52
4516 6643 0.458669 GGTTCATCCTAGCCGTCGAA 59.541 55.000 0.00 0.00 0.00 3.71
4524 6651 1.404986 CCTAGCCGTCGAACATGGAAA 60.405 52.381 0.00 0.00 31.73 3.13
4527 6654 0.098728 GCCGTCGAACATGGAAATGG 59.901 55.000 0.00 0.00 31.73 3.16
4532 6659 3.561310 CGTCGAACATGGAAATGGATGAT 59.439 43.478 0.00 0.00 0.00 2.45
4536 6663 5.297527 TCGAACATGGAAATGGATGATCTTG 59.702 40.000 0.00 0.00 0.00 3.02
4540 6667 6.903516 ACATGGAAATGGATGATCTTGTAGA 58.096 36.000 0.00 0.00 0.00 2.59
4542 6669 8.003044 ACATGGAAATGGATGATCTTGTAGATT 58.997 33.333 0.00 0.00 34.53 2.40
4547 6674 7.814264 AATGGATGATCTTGTAGATTCCAAC 57.186 36.000 11.94 0.00 42.04 3.77
4548 6675 5.684704 TGGATGATCTTGTAGATTCCAACC 58.315 41.667 7.36 3.82 38.20 3.77
4549 6676 5.429762 TGGATGATCTTGTAGATTCCAACCT 59.570 40.000 7.36 0.00 38.20 3.50
4551 6678 6.261826 GGATGATCTTGTAGATTCCAACCTTG 59.738 42.308 0.00 0.00 34.53 3.61
4556 6683 6.240292 ATCTTGTAGATTCCAACCTTGAAGGT 60.240 38.462 11.91 11.91 40.58 3.50
4557 6684 8.230480 ATCTTGTAGATTCCAACCTTGAAGGTG 61.230 40.741 19.04 11.73 38.75 4.00
4571 6698 3.743521 TGAAGGTGTTGATGAGGTCTTG 58.256 45.455 0.00 0.00 0.00 3.02
4661 6795 8.495260 CCCTTCTACCCTTCTAAATAAATGTCT 58.505 37.037 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
195 216 1.844497 GGTAGTACCAGCCAAATCCCT 59.156 52.381 14.82 0.00 38.42 4.20
239 267 4.881273 GGGCTTTGTTGGAAATTTCAAAGT 59.119 37.500 19.49 0.00 44.57 2.66
250 278 0.257328 TGTCACAGGGCTTTGTTGGA 59.743 50.000 0.00 0.00 0.00 3.53
263 291 2.205911 TCTTTCGCGAACAATGTCACA 58.794 42.857 23.33 2.07 0.00 3.58
264 292 2.941891 TCTTTCGCGAACAATGTCAC 57.058 45.000 23.33 0.00 0.00 3.67
506 535 1.901650 GAGACAAAGCCAGGCGAACG 61.902 60.000 5.55 0.00 0.00 3.95
669 799 0.241213 TGCAGACAGAGCAGTCGTAC 59.759 55.000 0.00 0.00 43.24 3.67
702 832 0.377203 CTACGCGGCAAAATTCTCCC 59.623 55.000 12.47 0.00 0.00 4.30
713 843 2.274920 AGTAGAAAACTCTACGCGGC 57.725 50.000 12.47 0.00 45.23 6.53
723 853 9.406828 CCCTTTGTTTAAGCAATAGTAGAAAAC 57.593 33.333 5.52 0.00 32.19 2.43
765 2373 4.538738 AGGTACACTCAATCCTCTCCTAC 58.461 47.826 0.00 0.00 0.00 3.18
846 2454 1.227089 CAATCCGCTCCAGACGAGG 60.227 63.158 0.00 0.00 39.22 4.63
914 2532 1.215647 CGGGTCAAGACTTCGGAGG 59.784 63.158 0.00 0.00 0.00 4.30
918 2536 0.319555 TTGCTCGGGTCAAGACTTCG 60.320 55.000 0.00 5.39 0.00 3.79
927 2545 0.460459 GCCTACTTCTTGCTCGGGTC 60.460 60.000 0.00 0.00 0.00 4.46
950 2568 1.549203 AACTAACAGCAAGCCATGGG 58.451 50.000 15.13 0.00 0.00 4.00
984 2602 0.178967 TCATCAAAGCCCCTTGCACA 60.179 50.000 0.00 0.00 44.83 4.57
986 2604 1.187974 CATCATCAAAGCCCCTTGCA 58.812 50.000 0.00 0.00 44.83 4.08
1015 2633 3.113191 TGCTTCTCCCTCATCTCTCTT 57.887 47.619 0.00 0.00 0.00 2.85
1053 2671 2.821810 GCTTCTCCTTCCTGCCGC 60.822 66.667 0.00 0.00 0.00 6.53
1093 2711 0.827925 TTCTCTCCTGTCACTGCCGT 60.828 55.000 0.00 0.00 0.00 5.68
1100 2718 1.006519 CCTCTCCCTTCTCTCCTGTCA 59.993 57.143 0.00 0.00 0.00 3.58
1122 2752 2.383855 CTTTCTCCGTCATCCCTCTCT 58.616 52.381 0.00 0.00 0.00 3.10
1168 2798 1.676006 CTCTTCTTCCTCCTCGCTCTC 59.324 57.143 0.00 0.00 0.00 3.20
1190 2820 3.326297 CACCTTGTCTTTCTTCTCCTCCT 59.674 47.826 0.00 0.00 0.00 3.69
1234 2864 3.032609 CGCGATCGCCAGCCTTAG 61.033 66.667 32.63 13.42 37.98 2.18
1378 3008 4.680440 GCCAAATGAACACCAAAACAGAGT 60.680 41.667 0.00 0.00 0.00 3.24
1379 3009 3.803778 GCCAAATGAACACCAAAACAGAG 59.196 43.478 0.00 0.00 0.00 3.35
1380 3010 3.196469 TGCCAAATGAACACCAAAACAGA 59.804 39.130 0.00 0.00 0.00 3.41
1381 3011 3.529533 TGCCAAATGAACACCAAAACAG 58.470 40.909 0.00 0.00 0.00 3.16
1406 3075 4.760204 ACCGATCGAACCAAAAGAAGAAAT 59.240 37.500 18.66 0.00 0.00 2.17
1444 3122 1.242076 AGCCAAAGATGCACAGACAC 58.758 50.000 0.00 0.00 0.00 3.67
1448 3126 2.400399 CAACAAGCCAAAGATGCACAG 58.600 47.619 0.00 0.00 0.00 3.66
1449 3127 1.538634 GCAACAAGCCAAAGATGCACA 60.539 47.619 0.00 0.00 37.23 4.57
1450 3128 1.142474 GCAACAAGCCAAAGATGCAC 58.858 50.000 0.00 0.00 37.23 4.57
1463 3141 1.070786 GTGGACGGGAGAGCAACAA 59.929 57.895 0.00 0.00 0.00 2.83
1598 3277 2.924302 TGAGGGTGGGAAGAGAGTAGTA 59.076 50.000 0.00 0.00 0.00 1.82
1605 3284 1.190643 GAGAGTGAGGGTGGGAAGAG 58.809 60.000 0.00 0.00 0.00 2.85
1606 3285 0.612174 CGAGAGTGAGGGTGGGAAGA 60.612 60.000 0.00 0.00 0.00 2.87
1607 3286 1.608717 CCGAGAGTGAGGGTGGGAAG 61.609 65.000 0.00 0.00 0.00 3.46
1608 3287 1.609501 CCGAGAGTGAGGGTGGGAA 60.610 63.158 0.00 0.00 0.00 3.97
1609 3288 2.037367 CCGAGAGTGAGGGTGGGA 59.963 66.667 0.00 0.00 0.00 4.37
1610 3289 3.077556 CCCGAGAGTGAGGGTGGG 61.078 72.222 0.00 0.00 42.67 4.61
1611 3290 3.077556 CCCCGAGAGTGAGGGTGG 61.078 72.222 0.00 0.00 46.17 4.61
1633 3331 5.348986 TCCTAGTGGTACGTACTACTTACG 58.651 45.833 38.50 27.85 44.19 3.18
1634 3332 6.819146 AGTTCCTAGTGGTACGTACTACTTAC 59.181 42.308 38.50 29.59 44.19 2.34
1635 3333 6.947464 AGTTCCTAGTGGTACGTACTACTTA 58.053 40.000 38.50 25.40 44.19 2.24
1636 3334 5.810095 AGTTCCTAGTGGTACGTACTACTT 58.190 41.667 38.50 25.86 44.19 2.24
1637 3335 6.155393 ACTAGTTCCTAGTGGTACGTACTACT 59.845 42.308 36.51 36.51 44.47 2.57
1638 3336 6.342111 ACTAGTTCCTAGTGGTACGTACTAC 58.658 44.000 28.78 28.78 44.47 2.73
1639 3337 6.546428 ACTAGTTCCTAGTGGTACGTACTA 57.454 41.667 24.07 16.71 44.47 1.82
1640 3338 5.428184 ACTAGTTCCTAGTGGTACGTACT 57.572 43.478 24.07 10.11 44.47 2.73
1650 3348 4.778579 TCGCTGATACACTAGTTCCTAGT 58.221 43.478 0.00 0.00 46.75 2.57
1651 3349 5.703592 AGATCGCTGATACACTAGTTCCTAG 59.296 44.000 0.00 0.00 39.72 3.02
1652 3350 5.622180 AGATCGCTGATACACTAGTTCCTA 58.378 41.667 0.00 0.00 0.00 2.94
1653 3351 4.465886 AGATCGCTGATACACTAGTTCCT 58.534 43.478 0.00 0.00 0.00 3.36
1654 3352 4.839668 AGATCGCTGATACACTAGTTCC 57.160 45.455 0.00 0.00 0.00 3.62
1655 3353 5.180492 AGCTAGATCGCTGATACACTAGTTC 59.820 44.000 0.00 0.00 39.16 3.01
1656 3354 5.067273 AGCTAGATCGCTGATACACTAGTT 58.933 41.667 0.00 0.00 39.16 2.24
1657 3355 4.647611 AGCTAGATCGCTGATACACTAGT 58.352 43.478 0.00 0.00 39.16 2.57
1658 3356 6.729391 TTAGCTAGATCGCTGATACACTAG 57.271 41.667 5.46 0.00 41.12 2.57
1659 3357 7.689446 ATTTAGCTAGATCGCTGATACACTA 57.311 36.000 5.46 0.00 41.12 2.74
1660 3358 6.582677 ATTTAGCTAGATCGCTGATACACT 57.417 37.500 5.46 0.00 41.12 3.55
1661 3359 6.400515 GCAATTTAGCTAGATCGCTGATACAC 60.401 42.308 0.05 0.00 41.12 2.90
1662 3360 5.635280 GCAATTTAGCTAGATCGCTGATACA 59.365 40.000 0.05 0.00 41.12 2.29
1663 3361 5.866633 AGCAATTTAGCTAGATCGCTGATAC 59.133 40.000 8.81 0.00 44.50 2.24
1664 3362 5.866092 CAGCAATTTAGCTAGATCGCTGATA 59.134 40.000 25.57 0.00 46.56 2.15
1665 3363 4.689812 CAGCAATTTAGCTAGATCGCTGAT 59.310 41.667 25.57 5.54 46.56 2.90
1688 3388 4.381566 CGTGCATGTTTAGTTTTTACCAGC 59.618 41.667 0.00 0.00 0.00 4.85
1689 3389 5.753744 TCGTGCATGTTTAGTTTTTACCAG 58.246 37.500 5.68 0.00 0.00 4.00
1691 3391 5.116528 GCTTCGTGCATGTTTAGTTTTTACC 59.883 40.000 5.68 0.00 42.31 2.85
1708 3410 1.469940 CCTGCCTACTACTGCTTCGTG 60.470 57.143 0.00 0.00 0.00 4.35
1711 3413 1.410882 CTCCCTGCCTACTACTGCTTC 59.589 57.143 0.00 0.00 0.00 3.86
1712 3414 1.273324 ACTCCCTGCCTACTACTGCTT 60.273 52.381 0.00 0.00 0.00 3.91
1713 3415 0.336737 ACTCCCTGCCTACTACTGCT 59.663 55.000 0.00 0.00 0.00 4.24
1714 3416 0.747852 GACTCCCTGCCTACTACTGC 59.252 60.000 0.00 0.00 0.00 4.40
1715 3417 2.303175 GAGACTCCCTGCCTACTACTG 58.697 57.143 0.00 0.00 0.00 2.74
1716 3418 1.134037 CGAGACTCCCTGCCTACTACT 60.134 57.143 0.00 0.00 0.00 2.57
1717 3419 1.134159 TCGAGACTCCCTGCCTACTAC 60.134 57.143 0.00 0.00 0.00 2.73
1718 3420 1.210538 TCGAGACTCCCTGCCTACTA 58.789 55.000 0.00 0.00 0.00 1.82
1730 3432 0.333312 AGAGGGGTGTGATCGAGACT 59.667 55.000 0.00 0.00 0.00 3.24
1746 3448 4.026744 TGGATCTTTGGTCTCAGGTAGAG 58.973 47.826 0.00 0.00 46.14 2.43
1747 3449 4.061131 TGGATCTTTGGTCTCAGGTAGA 57.939 45.455 0.00 0.00 0.00 2.59
1763 3465 4.437930 CGACTTGCCATCTTCTTTTGGATC 60.438 45.833 0.00 0.00 34.81 3.36
1774 3476 0.976641 TTGGAGTCGACTTGCCATCT 59.023 50.000 22.61 0.00 0.00 2.90
1788 3490 5.496133 AGAAATCTTGATGCGATTTGGAG 57.504 39.130 3.05 0.00 40.21 3.86
1856 3558 1.943340 GACGAGATGGATGGGAAAAGC 59.057 52.381 0.00 0.00 0.00 3.51
1919 3621 1.207488 TAAGCAGGCCACAGGGTGAT 61.207 55.000 5.01 0.00 35.23 3.06
1923 3626 1.560505 AAAATAAGCAGGCCACAGGG 58.439 50.000 5.01 0.00 37.18 4.45
1959 3662 8.983307 AAGTAGAATAACCACGCTTATATAGC 57.017 34.615 0.00 0.00 46.83 2.97
1967 3670 9.836076 GAAAATAAAAAGTAGAATAACCACGCT 57.164 29.630 0.00 0.00 0.00 5.07
1968 3671 9.836076 AGAAAATAAAAAGTAGAATAACCACGC 57.164 29.630 0.00 0.00 0.00 5.34
1981 3684 8.360390 CCAGGCTAAACTCAGAAAATAAAAAGT 58.640 33.333 0.00 0.00 0.00 2.66
1982 3685 8.360390 ACCAGGCTAAACTCAGAAAATAAAAAG 58.640 33.333 0.00 0.00 0.00 2.27
1983 3686 8.245195 ACCAGGCTAAACTCAGAAAATAAAAA 57.755 30.769 0.00 0.00 0.00 1.94
1984 3687 7.833285 ACCAGGCTAAACTCAGAAAATAAAA 57.167 32.000 0.00 0.00 0.00 1.52
1985 3688 7.833285 AACCAGGCTAAACTCAGAAAATAAA 57.167 32.000 0.00 0.00 0.00 1.40
1986 3689 9.528489 AATAACCAGGCTAAACTCAGAAAATAA 57.472 29.630 0.00 0.00 0.00 1.40
1991 3694 9.832445 CTAATAATAACCAGGCTAAACTCAGAA 57.168 33.333 0.00 0.00 0.00 3.02
2066 3894 3.426117 ATCGGGTGATGCGTCGGAC 62.426 63.158 0.58 0.00 32.21 4.79
2071 3899 0.828022 TAAAGGATCGGGTGATGCGT 59.172 50.000 0.00 0.00 46.58 5.24
2089 3917 0.443869 GTAAGACGACGGCGACAGTA 59.556 55.000 22.49 4.84 41.64 2.74
2090 3918 1.208614 GTAAGACGACGGCGACAGT 59.791 57.895 22.49 10.37 41.64 3.55
2149 3978 1.269102 CCGATCAAACTATCGCGGTCT 60.269 52.381 6.13 0.00 45.79 3.85
2162 3991 0.392706 CCGTCCCATGATCCGATCAA 59.607 55.000 14.99 0.00 43.50 2.57
2268 4129 4.637534 CGGAGATATTTGCCTAATCCCATG 59.362 45.833 0.00 0.00 0.00 3.66
2289 4150 3.971032 AAGCAAAAGTTGTCTTCTCGG 57.029 42.857 0.00 0.00 32.90 4.63
2337 4201 1.420138 CACGACCCCCTAATGCCTAAT 59.580 52.381 0.00 0.00 0.00 1.73
2338 4202 0.834612 CACGACCCCCTAATGCCTAA 59.165 55.000 0.00 0.00 0.00 2.69
2339 4203 0.325860 ACACGACCCCCTAATGCCTA 60.326 55.000 0.00 0.00 0.00 3.93
2340 4204 1.615424 ACACGACCCCCTAATGCCT 60.615 57.895 0.00 0.00 0.00 4.75
2341 4205 1.451387 CACACGACCCCCTAATGCC 60.451 63.158 0.00 0.00 0.00 4.40
2342 4206 2.112815 GCACACGACCCCCTAATGC 61.113 63.158 0.00 0.00 0.00 3.56
2343 4207 1.451387 GGCACACGACCCCCTAATG 60.451 63.158 0.00 0.00 0.00 1.90
2415 4279 0.533032 AACGGACAAGAGAGCTAGCC 59.467 55.000 12.13 2.81 0.00 3.93
2611 4492 1.012486 CAGTAAGTTCGTGCCGTCCC 61.012 60.000 0.00 0.00 0.00 4.46
2612 4493 0.319297 ACAGTAAGTTCGTGCCGTCC 60.319 55.000 0.00 0.00 0.00 4.79
2617 4498 4.791974 ACAGTACTACAGTAAGTTCGTGC 58.208 43.478 0.00 0.00 31.52 5.34
2636 4517 4.330074 CCGAAGTTTCAGCCTAACATACAG 59.670 45.833 0.00 0.00 0.00 2.74
2638 4519 3.621715 CCCGAAGTTTCAGCCTAACATAC 59.378 47.826 0.00 0.00 0.00 2.39
2641 4522 1.695242 TCCCGAAGTTTCAGCCTAACA 59.305 47.619 0.00 0.00 0.00 2.41
2642 4523 2.467566 TCCCGAAGTTTCAGCCTAAC 57.532 50.000 0.00 0.00 0.00 2.34
2727 4611 6.321945 TCAATGCTGAATTAGGTGTTGCATAT 59.678 34.615 0.00 0.00 38.49 1.78
2767 4652 7.016296 TCAAAACATTTTAAGAAGGGGGAGAT 58.984 34.615 0.00 0.00 0.00 2.75
2942 4829 0.179194 CGTCGTCGGTCTCTTTCTCC 60.179 60.000 0.00 0.00 0.00 3.71
2993 4880 3.835395 ACCTAGTGAGCCATAGAATAGCC 59.165 47.826 0.00 0.00 0.00 3.93
3028 4915 8.887036 ATAGAACGTCAATATAAGTTGCATCA 57.113 30.769 0.00 0.00 0.00 3.07
3039 4926 9.151471 GCACAATGGTATATAGAACGTCAATAT 57.849 33.333 0.00 0.00 0.00 1.28
3057 4953 5.893687 TGCATTAATCAAGTAGCACAATGG 58.106 37.500 0.00 0.00 0.00 3.16
3120 5018 5.434408 CAACAGAGAAATCCATGGATCTGA 58.566 41.667 34.44 10.80 33.08 3.27
3137 5035 3.384789 AGTCTCTGTAACAGTGCAACAGA 59.615 43.478 20.87 20.87 45.48 3.41
3208 5121 1.616865 ACCTTGTACGCAGCTTCTACA 59.383 47.619 0.00 0.00 0.00 2.74
3241 5154 1.135721 GAAGAAATCCAGCCATGCCAC 59.864 52.381 0.00 0.00 0.00 5.01
3283 5196 4.037858 AGCTGAAAAACAAACTGAGCAG 57.962 40.909 0.00 0.00 0.00 4.24
3286 5199 4.024893 TCGCTAGCTGAAAAACAAACTGAG 60.025 41.667 13.93 0.00 0.00 3.35
3318 5233 1.009389 CGTCTGTCTGTCGGGCTTTC 61.009 60.000 0.00 0.00 0.00 2.62
3319 5234 1.006102 CGTCTGTCTGTCGGGCTTT 60.006 57.895 0.00 0.00 0.00 3.51
3320 5235 2.651361 CGTCTGTCTGTCGGGCTT 59.349 61.111 0.00 0.00 0.00 4.35
3321 5236 4.057428 GCGTCTGTCTGTCGGGCT 62.057 66.667 0.00 0.00 0.00 5.19
3322 5237 3.575351 AAGCGTCTGTCTGTCGGGC 62.575 63.158 0.00 0.00 0.00 6.13
3323 5238 1.734477 CAAGCGTCTGTCTGTCGGG 60.734 63.158 0.00 0.00 0.00 5.14
3324 5239 1.004277 GACAAGCGTCTGTCTGTCGG 61.004 60.000 10.63 0.00 42.11 4.79
3325 5240 1.004277 GGACAAGCGTCTGTCTGTCG 61.004 60.000 15.60 0.00 44.33 4.35
3326 5241 0.315568 AGGACAAGCGTCTGTCTGTC 59.684 55.000 15.60 9.22 44.33 3.51
3327 5242 0.032678 CAGGACAAGCGTCTGTCTGT 59.967 55.000 15.60 1.86 44.33 3.41
3328 5243 0.315251 TCAGGACAAGCGTCTGTCTG 59.685 55.000 15.60 12.35 44.33 3.51
3329 5244 1.261480 ATCAGGACAAGCGTCTGTCT 58.739 50.000 15.60 3.33 44.33 3.41
3330 5245 2.924290 GTTATCAGGACAAGCGTCTGTC 59.076 50.000 9.70 9.70 44.21 3.51
3337 5252 3.412386 ACCAAGTGTTATCAGGACAAGC 58.588 45.455 0.00 0.00 0.00 4.01
3354 5269 2.937469 CAGTTGTGCAAGTCAACCAA 57.063 45.000 13.37 0.00 44.02 3.67
3371 5286 6.321717 TCTGTTTCAACAAAGTTTGTAGCAG 58.678 36.000 21.14 20.30 44.59 4.24
3374 5289 6.140737 GCGATCTGTTTCAACAAAGTTTGTAG 59.859 38.462 21.14 13.48 44.59 2.74
3471 5386 1.932511 GCTTCTCAATCTCGAGCTTGG 59.067 52.381 24.45 16.58 32.75 3.61
3592 5509 7.224753 CGCATAACTCATACTGTCATTTAAGGT 59.775 37.037 0.00 0.00 0.00 3.50
3593 5510 7.438160 TCGCATAACTCATACTGTCATTTAAGG 59.562 37.037 0.00 0.00 0.00 2.69
3624 5544 3.819902 TCACACAGCAATGCTTAATCACA 59.180 39.130 4.36 0.00 36.40 3.58
3648 5569 3.066203 AGTTTGAACTTGGCCTGTAAACG 59.934 43.478 3.32 0.00 35.21 3.60
3696 5617 5.378230 AATGGAGACCATCTTAGCATTCA 57.622 39.130 3.69 0.00 44.40 2.57
4008 5974 6.000219 TCTGAATTCAGGGCTAATTCATAGC 59.000 40.000 30.33 0.00 46.65 2.97
4037 6003 2.612672 GCGATAGAAACCCTAGCAAACC 59.387 50.000 0.00 0.00 33.51 3.27
4038 6004 3.532542 AGCGATAGAAACCCTAGCAAAC 58.467 45.455 0.00 0.00 33.51 2.93
4056 6022 5.349824 AGCTTTACTTTTCTCTTTGAGCG 57.650 39.130 0.00 0.00 33.15 5.03
4071 6037 2.271800 CTGATGTGGGTCGAGCTTTAC 58.728 52.381 15.18 11.62 0.00 2.01
4172 6297 5.367302 ACAAAACAGGGAATGTCAAAATGG 58.633 37.500 0.00 0.00 43.00 3.16
4215 6340 9.821240 ATGTTCTATATGACATAGAGAAGGAGT 57.179 33.333 25.64 13.32 41.97 3.85
4242 6367 7.118535 GTCTCTACCTTTAGCTTCTCTTTTTGG 59.881 40.741 0.00 0.00 0.00 3.28
4248 6373 4.936802 TGGTCTCTACCTTTAGCTTCTCT 58.063 43.478 0.00 0.00 46.91 3.10
4277 6402 0.531974 GCACACGTCTCCCAACTCAA 60.532 55.000 0.00 0.00 0.00 3.02
4291 6416 2.352805 CCCCTCCCTCTTGCACAC 59.647 66.667 0.00 0.00 0.00 3.82
4299 6424 1.925972 AAAGCTCACCCCCTCCCTC 60.926 63.158 0.00 0.00 0.00 4.30
4301 6426 2.356667 CAAAGCTCACCCCCTCCC 59.643 66.667 0.00 0.00 0.00 4.30
4357 6482 8.680001 TCCAGTTTTGTCTCTTTTACTTTTACC 58.320 33.333 0.00 0.00 0.00 2.85
4360 6485 9.419297 GTTTCCAGTTTTGTCTCTTTTACTTTT 57.581 29.630 0.00 0.00 0.00 2.27
4361 6486 7.753580 CGTTTCCAGTTTTGTCTCTTTTACTTT 59.246 33.333 0.00 0.00 0.00 2.66
4362 6487 7.120138 TCGTTTCCAGTTTTGTCTCTTTTACTT 59.880 33.333 0.00 0.00 0.00 2.24
4378 6503 2.628178 TGTCTCTCATGTCGTTTCCAGT 59.372 45.455 0.00 0.00 0.00 4.00
4382 6507 8.535592 CATTTACTATGTCTCTCATGTCGTTTC 58.464 37.037 0.00 0.00 37.91 2.78
4387 6512 7.148836 CGCATCATTTACTATGTCTCTCATGTC 60.149 40.741 0.00 0.00 37.91 3.06
4388 6513 6.644181 CGCATCATTTACTATGTCTCTCATGT 59.356 38.462 0.00 0.00 37.91 3.21
4398 6523 7.946655 TTTACCTCTCGCATCATTTACTATG 57.053 36.000 0.00 0.00 0.00 2.23
4409 6534 3.821033 GGGCATTTATTTACCTCTCGCAT 59.179 43.478 0.00 0.00 0.00 4.73
4422 6549 3.360867 TCATCCAACAACGGGCATTTAT 58.639 40.909 0.00 0.00 0.00 1.40
4453 6580 0.039798 TAAGTGACGACGTGGACAGC 60.040 55.000 4.58 0.00 0.00 4.40
4456 6583 2.412421 ACTTAAGTGACGACGTGGAC 57.588 50.000 4.58 1.42 0.00 4.02
4468 6595 2.413837 CAGTACGCAAGCCACTTAAGT 58.586 47.619 1.12 1.12 45.62 2.24
4482 6609 3.578515 AACCGGGCGAACCAGTACG 62.579 63.158 6.32 0.00 40.22 3.67
4484 6611 1.546589 ATGAACCGGGCGAACCAGTA 61.547 55.000 6.32 0.00 40.22 2.74
4488 6615 1.963464 TAGGATGAACCGGGCGAACC 61.963 60.000 6.32 3.57 44.74 3.62
4497 6624 0.458669 TTCGACGGCTAGGATGAACC 59.541 55.000 0.00 0.00 39.35 3.62
4498 6625 1.135199 TGTTCGACGGCTAGGATGAAC 60.135 52.381 0.00 0.00 36.98 3.18
4511 6638 4.818546 AGATCATCCATTTCCATGTTCGAC 59.181 41.667 0.00 0.00 0.00 4.20
4516 6643 6.903516 TCTACAAGATCATCCATTTCCATGT 58.096 36.000 0.00 0.00 0.00 3.21
4524 6651 6.102321 AGGTTGGAATCTACAAGATCATCCAT 59.898 38.462 9.91 0.00 39.85 3.41
4527 6654 7.050377 TCAAGGTTGGAATCTACAAGATCATC 58.950 38.462 0.00 0.00 32.89 2.92
4532 6659 5.560724 CCTTCAAGGTTGGAATCTACAAGA 58.439 41.667 0.00 0.00 0.00 3.02
4547 6674 3.077359 GACCTCATCAACACCTTCAAGG 58.923 50.000 0.22 0.22 42.49 3.61
4548 6675 4.013267 AGACCTCATCAACACCTTCAAG 57.987 45.455 0.00 0.00 0.00 3.02
4549 6676 4.136796 CAAGACCTCATCAACACCTTCAA 58.863 43.478 0.00 0.00 0.00 2.69
4551 6678 3.748568 GTCAAGACCTCATCAACACCTTC 59.251 47.826 0.00 0.00 0.00 3.46
4556 6683 3.503363 GCATTGTCAAGACCTCATCAACA 59.497 43.478 0.00 0.00 0.00 3.33
4557 6684 3.119708 GGCATTGTCAAGACCTCATCAAC 60.120 47.826 0.00 0.00 0.00 3.18
4560 6687 2.019984 GGGCATTGTCAAGACCTCATC 58.980 52.381 6.61 0.00 0.00 2.92
4561 6688 1.341383 GGGGCATTGTCAAGACCTCAT 60.341 52.381 6.80 0.00 0.00 2.90
4563 6690 0.681243 GGGGGCATTGTCAAGACCTC 60.681 60.000 6.80 3.16 0.00 3.85
4602 6736 3.345508 TCAGCCTCGAGTACAAGACTA 57.654 47.619 12.31 0.00 39.06 2.59
4661 6795 3.904339 GAGGATGCTAAATGGGAGGACTA 59.096 47.826 0.00 0.00 0.00 2.59


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.